Molecular Biology Basics
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Questions and Answers

What is the primary function of DNA polymerase?

  • To catalyze the joining of amino acids
  • To modify and transport proteins
  • To unzip the DNA double helix
  • To catalyze the joining of deoxyribonucleotide triphosphates (correct)

During which phase of the cell cycle does DNA replication occur?

  • S Phase (correct)
  • G2 Phase
  • M Phase
  • G1 Phase

What are the complementary base pairs in DNA?

  • A-C; T-G
  • G-C; T-A
  • A-T; G-C (correct)
  • C-T; A-G

Which cellular compartment is primarily responsible for translation?

<p>Rough Endoplasmic Reticulum (D)</p> Signup and view all the answers

What role do Clamp-loading proteins play during DNA replication?

<p>To coordinate leading and lagging strands synthesis (C)</p> Signup and view all the answers

Which process converts pre-mRNA into mRNA?

<p>Splicing (D)</p> Signup and view all the answers

What occurs to misfolded proteins in the cytoplasm?

<p>They are degraded (D)</p> Signup and view all the answers

What is the main structure of DNA?

<p>Double helix formed by complementary strands (C)</p> Signup and view all the answers

What is the direction of DNA synthesis by all DNA Polymerases?

<p>5′ to 3′ (A)</p> Signup and view all the answers

What is required for DNA polymerase to synthesize DNA?

<p>A primer strand bonded to a template (C)</p> Signup and view all the answers

What is the role of DNA Primase in DNA replication?

<p>To produce short RNA fragments that act as primers (A)</p> Signup and view all the answers

What reduces the error rate during DNA replication?

<p>Base-pairing of correctly matched dNTPs (A)</p> Signup and view all the answers

What determines the expression of the lac operon?

<p>Combined action of activators and repressors (C)</p> Signup and view all the answers

What are Okazaki fragments?

<p>Short DNA segments synthesized on the lagging strand (C)</p> Signup and view all the answers

In the lac operon, what is the role of the i gene?

<p>It encodes a repressor that binds to the operator (D)</p> Signup and view all the answers

How does telomerase maintain telomeres?

<p>By catalyzing synthesis using its RNA template (D)</p> Signup and view all the answers

What happens when DNA primase removes the RNA primer?

<p>An overhanging 3′ end is created (B)</p> Signup and view all the answers

What happens to cAMP levels when glucose levels decrease?

<p>cAMP levels increase (B)</p> Signup and view all the answers

What is the main challenge that the lagging strand faces during DNA replication?

<p>Synthesis in the opposite direction of the overall replication fork (C)</p> Signup and view all the answers

Which statement best describes the mechanism of enhancers in gene regulation?

<p>Enhancers can act over long distances by bending DNA (C)</p> Signup and view all the answers

What complicates transcription in eukaryotic cells?

<p>The presence of histone proteins and nucleosomes (D)</p> Signup and view all the answers

What is the primary function of promoters in eukaryotic transcription?

<p>To serve as binding sites for general transcription factors (B)</p> Signup and view all the answers

In the absence of lactose, what is the state of the repressor protein in the lac operon?

<p>It binds to the operator to inhibit transcription (A)</p> Signup and view all the answers

How does positive control affect the regulation of the lac operon?

<p>By facilitating the binding of CAP by increasing cAMP levels (B)</p> Signup and view all the answers

What is the primary reason bacterial mRNAs are used immediately for protein synthesis?

<p>Bacteria lack mRNA processing mechanisms. (B)</p> Signup and view all the answers

What is the role of the tryptophan repressor in bacterial gene regulation?

<p>It inhibits the binding of RNA polymerase to the promoter. (D)</p> Signup and view all the answers

Which statement accurately describes mRNA regulation in eukaryotes compared to bacteria?

<p>Eukaryotic mRNA must be exported to the cytoplasm for translation. (D)</p> Signup and view all the answers

What is the mechanism by which bacterial cells adapt to environmental changes concerning gene expression?

<p>Via transcriptional regulation that works primarily at the initiation step. (D)</p> Signup and view all the answers

Which enzyme is responsible for cleaving lactose into glucose and galactose?

<p>Beta-galactosidase (A)</p> Signup and view all the answers

What do operons allow bacteria to do in terms of gene expression?

<p>Control clusters of genes with a single promoter. (A)</p> Signup and view all the answers

How does the half-life of bacterial mRNA compare to that of eukaryotic mRNA?

<p>Bacterial mRNA typically has a much shorter half-life. (C)</p> Signup and view all the answers

Which of the following describes the primary function of the Lac Operon?

<p>To regulate the synthesis of enzymes that metabolize lactose. (A)</p> Signup and view all the answers

What role does DNA looping play in gene regulation?

<p>It facilitates interaction between a transcription factor at an enhancer and the RNA polymerase/Mediator complex at the promoter. (D)</p> Signup and view all the answers

Which component is primarily responsible for recognizing intron-exon boundaries during pre-mRNA splicing?

<p>snRNPs (C)</p> Signup and view all the answers

What is alternative splicing?

<p>A method that produces different mRNA variants from a single gene by including or excluding specific exons. (B)</p> Signup and view all the answers

Which of the following best describes the function of the spliceosome?

<p>It catalyzes the splicing of introns from pre-mRNA. (B)</p> Signup and view all the answers

Which of the following tissues produces calcitonin gene-related peptide (CGRP)?

<p>Hypothalamus (C)</p> Signup and view all the answers

What happens to the signal sequence during cotranslational targeting of secretory proteins to the ER?

<p>It is cleaved by signal peptidase and released into the ER lumen. (C)</p> Signup and view all the answers

During the elongation phase of translation, which site on the ribosome does an aminoacyl tRNA first bind to?

<p>A site (A)</p> Signup and view all the answers

Which factor is critical for bringing aminoacyl tRNA to the ribosome during elongation?

<p>GTP-bound elongation factors (D)</p> Signup and view all the answers

What role does rRNA play during the peptide bond formation?

<p>It mediates the formation of the peptide bond. (B)</p> Signup and view all the answers

Which factor is involved in the translocation step of elongation in prokaryotes?

<p>EF-G (B)</p> Signup and view all the answers

What is the primary function of Dicer in the processing of microRNA?

<p>It creates the functional form of miRNA. (B)</p> Signup and view all the answers

What potential consequence can arise from defective protein folding?

<p>Formation of protein aggregates. (B)</p> Signup and view all the answers

Which of the following is a known role of miRNAs in cellular regulation?

<p>Repressing the translation of specific mRNAs. (B)</p> Signup and view all the answers

Which miRNA is specifically mentioned as repressing the translation of Lin-14?

<p>Lin-4 (D)</p> Signup and view all the answers

How many different mRNAs can a single miRNA potentially target?

<p>Up to 100 (A)</p> Signup and view all the answers

What is one of the diseases associated with misfolded proteins in the brain?

<p>Alzheimer’s disease (A)</p> Signup and view all the answers

Flashcards

DNA Structure

DNA is a nucleic acid made of nucleotides, deoxyribose sugar, phosphate group, and nitrogenous bases (adenine, thymine, cytosine, guanine).

Central Dogma

Information flows from DNA to RNA to protein.

DNA Replication

The process of copying DNA before cell division.

DNA Polymerase

The enzyme that builds new DNA strands during replication.

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Complementary Base Pairing

A-T and G-C pairings in DNA.

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Transcription

The process of making RNA from DNA.

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Translation

The process of making protein from RNA.

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Nucleic Acids

Biological molecules that carry genetic information

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DNA Polymerase Direction

DNA polymerases can only add nucleotides to the 3' end of a growing DNA strand. They can't start a new strand, they can only extend an existing one.

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DNA Polymerase Primer

DNA polymerases need a short, pre-existing strand of RNA called a primer to start adding nucleotides. They cannot start a new strand from scratch.

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How does DNA Replication Start?

RNA primase synthesizes short RNA primers that provide a starting point for DNA polymerase to begin replicating DNA.

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Leading Strand

The leading strand of DNA is synthesized continuously in the 5' to 3' direction, following the direction of the replication fork.

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Lagging Strand

The lagging strand is synthesized discontinuously in short fragments (Okazaki fragments), moving away from the replication fork.

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Okazaki Fragments

Short fragments of DNA synthesized on the lagging strand, which are later joined together by DNA ligase.

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Telomeres

Protective caps at the ends of linear chromosomes, composed of repeating sequences of DNA.

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Telomerase

An enzyme that adds repetitive DNA sequences to the ends of chromosomes (telomeres) to prevent shortening.

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mRNA Half-Life

The time it takes for an mRNA molecule to degrade in a cell. In bacteria, the half-life is short, around a few minutes. This allows for rapid changes in protein production based on environmental conditions.

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Transcription and Translation Separation

In eukaryotes, transcription (DNA to RNA) occurs in the nucleus, while translation (RNA to protein) happens in the cytoplasm. This physical separation allows for more complex regulation of gene expression.

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Gene Regulation

The process of controlling which genes are expressed (turned on) and at what level. This allows cells to adapt to different environmental conditions by producing the necessary proteins.

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Operator

A DNA sequence that binds to a repressor protein, regulating the transcription of nearby genes. It acts like a control switch for gene expression.

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Tryptophan Operon

A cluster of genes involved in tryptophan synthesis in bacteria. It's a classic example of a regulated operon, where the production of tryptophan enzymes is turned off when tryptophan levels are high.

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Repressor Protein

A protein that binds to an operator, blocking RNA polymerase from binding to the promoter and initiating transcription. It shuts down gene expression.

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Lac Operon

A cluster of genes in bacteria that code for enzymes involved in lactose metabolism. It's an example of an inducible operon, where the presence of lactose activates the expression of the genes.

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Inducible Operon

A type of operon that is switched on in the presence of a specific inducer molecule. For example, the Lac Operon is inducible by lactose.

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Lac Operon Control

The lac operon is regulated by both activators and repressors, ensuring lactose metabolism only when glucose is absent and lactose is present.

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Negative Control of Lac Operon

The lac operon is negatively controlled by the repressor protein, which binds to the operator site and blocks RNA polymerase from transcribing the genes involved in lactose metabolism.

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Positive Control of Lac Operon

The lac operon is positively controlled by the catabolite activator protein (CAP), which binds to DNA upstream of the promoter and enhances RNA polymerase binding.

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Eukaryotic Transcriptional Regulation

Transcriptional regulation in eukaryotes is more complex than in prokaryotes due to factors like chromatin structure, nuclear location of transcription, and a larger amount of regulatory DNA.

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Chromatin Structure

Eukaryotic DNA is packaged into chromatin, a complex of DNA, histones, and non-histone proteins, forming nucleosomes.

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Nucleosomes and Transcription

The compact structure of nucleosomes can restrict access of the transcription machinery to DNA, making transcription more challenging.

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Promoters

Promoters are DNA sequences that bind general transcription factors and mediate RNA polymerase II binding to initiate transcription.

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Enhancers

Enhancers are DNA sequences that bind specific transcription factors and can enhance transcription even when located far away from the promoter.

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Post-transcriptional regulation

The control of gene expression after transcription, affecting the processing, stability, and translation of mRNA.

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Introns

Non-coding regions of a gene that are removed from the pre-mRNA during splicing.

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Exons

Coding regions of a gene that are joined together to form the final mRNA.

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pre-mRNA splicing

A process where introns are removed from pre-mRNA and exons are joined together to produce mature mRNA.

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snRNPs

Small nuclear ribonucleoproteins that recognize intron-exon boundaries and participate in splicing.

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Spliceosome

A complex of snRNPs and proteins that catalyzes the excision of introns and the ligation of exons during splicing.

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Alternative splicing

A process that allows a single gene to produce multiple protein variants by including or excluding different exons during splicing.

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Tissue-specific splicing

Different tissues can produce distinct protein forms from the same gene through alternative splicing.

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Peptide Bond Formation

The carboxyl end of the polypeptide in the P site is joined to the free amino group of the amino acid in the A site, creating a peptide bond. This is facilitated by the rRNA of the large subunit.

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Translocation in Translation

The ribosome shifts three nucleotides along the mRNA, moving the next codon to the A site. The peptidyl tRNA moves from A to P, and the uncharged tRNA from P to E.

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Elongation Factors

Proteins that assist in the elongation phase of translation, such as EF-G/eEF2, which helps in translocation, and are involved in GTP hydrolysis.

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miRNA Function

MicroRNAs (miRNAs) regulate gene expression by binding to specific target mRNAs, often inhibiting their translation.

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RISC Complex

RNA-Induced Silencing Complex, a protein complex that contains miRNAs and plays a crucial role in silencing gene expression.

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Protein Folding Quality Control

Cells have mechanisms to ensure proper protein folding, guiding newly synthesized proteins into their correct three-dimensional structures.

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Protein Misfolding Consequences

Defective protein folding can lead to the formation of aggregates, which disrupt cellular function and contribute to diseases like Alzheimer's.

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Amyloid-β Plaques

Abnormal aggregates of amyloid-β protein found in the brain tissue of Alzheimer's patients, contributing to the development of the disease.

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Study Notes

DNA Structure

  • DNA is a nucleic acid composed of nucleotides.
  • Deoxyribose is a 5-carbon sugar.
  • A phosphate group (PO4) is attached to the 5' carbon of the sugar.
  • Nitrogenous bases include adenine, thymine, cytosine, and guanine.
  • A free hydroxyl group (-OH) is attached to the 3' carbon of the sugar.
  • Complementary base pairing: A-T; G-C
  • DNA forms a double helix from complementary strands.

Central Dogma

  • Information flows from DNA to RNA to protein.
  • Replication: DNA to DNA
  • Transcription: DNA to RNA
  • Translation: RNA to Proteins
  • These processes occur in different compartments of the cell.

DNA Replication

  • Every time a cell divides, its entire genome must be duplicated.
  • The process is quick and requires accuracy.
  • Watson and Crick postulated that DNA replication might be as simple as "unzipping" the helix and replacing the missing nucleotides.
  • DNA replication begins at discrete origins and then proceeds bidirectionally.

DNA Polymerase

  • DNA polymerase is the main enzyme in DNA replication.
  • It catalyzes the joining of deoxyribonucleotide 5'-triphosphates (dNTPs).
  • Discovered in E. coli in 1956 by Arthur Kornberg & colleagues using genetics and biochemistry.
  • Many different DNA polymerases exist in prokaryotes and eukaryotes. They play distinct roles in DNA replication and repair.
  • Several additional proteins are required for coordinated DNA synthesis.
  • These proteins include topoisomerase, helicase, primase, single-strand binding proteins, DNA polymerase III, DNA polymerase I, and ligase.

5' to 3' direction

  • DNA polymerases synthesize DNA only in the 5' to 3' direction.
  • They add new doxynucleotide triphosphates (dNTPs) only to a primer strand.
  • Primer strands are made of RNA.

DNA Primase

  • RNA primase synthesizes short RNA fragments that act as primers for DNA synthesis.
  • These short RNA primers then serve as primers for the extension of DNA.

Fidelity of DNA Replication

  • DNA polymerase helps to select the correct bases to insert during replication.
  • Binding correctly matched dNTPs causes conformational changes that lead to nucleotide incorporation.
  • Base pairing helps reduce the error rate to about 1 in 105 per nucleotide.

Leading and Lagging Strands

  • The leading strand is synthesized continuously in the 5' to 3' direction.
  • The lagging strand is synthesized discontinuously as short, fragments called Okazaki fragments.
  • Okazaki fragments are joined together by DNA ligase.

Telomeres and Telomerase

  • Linear chromosomes have specialized terminal sequences called telomeres. These contain repetitive DNA sequences.
  • Telomere sequences are maintained by the enzyme telomerase.
  • Telomerase is a reverse transcriptase whose RNA template is complementary to the telomere repeat sequences.
  • Removes the RNA primer, which may result in a staggered end.
  • Creates a loop in the telomere.

Transcription (DNA to RNA)

  • Prokaryotes: Transcription and translation occur in the same compartment.
  • Eukaryotes: Transcription occurs in the nucleus, and translation in the cytoplasm.
  • Several different RNA polymerases and various proteins are involved.
  • mRNA transcripts are translated much more quickly.
  • Bacterial mRNA has a very short half-life.

Transcription Regulation (bacteria)

  • Regulation of gene expression allows a bacterial cell to adapt to environmental changes such as food sources.
  • Most transcriptional regulation in bacteria operates at the initiation step.
  • In addition to the promoter, nearly all genes (bacterial and eukaryotic) have regulatory DNA sequences.
  • In bacteria, this sequence is commonly referred to as an operator.

Regulation of the Tryptophan Operon (an example of bacterial gene regulation)

  • Several proteins are needed to synthesize tryptophan, so the cell expresses them only when tryptophan is needed.
  • Genes that code for these proteins are clustered together as an operon (one unit).
  • The tryptophan operon is controlled by a strong promoter, and will bind RNA polymerase and transcribe the operon until it is repressed.
  • The operon is switched off by a repressor protein (tryptophan repressor).
  • The tryptophan repressor protein is responsive to tryptophan levels.

Lactose Metabolism

  • Genes encoding the enzymes involved in lactose metabolism are expressed as a single unit, the Lac operon.
  • Required enzymes: beta-galactosidase (z), lactose permease (y), and transacetylase (a).
  • Beta-galactosidase cleaves lactose into glucose and galactose.
  • Lactose permease transports lactose into the cell.
  • Transacetylase inactivates toxic thiogalactosides along with lactose.

Regulation of the Lac Operon

  • The combination of activators and repressors control the lac operon.
  • These enzymes are expressed only when glucose is absent and lactose is present.
  • Two loci control transcription: (operator), adjacent to transcription initiation site, and i (i gene, not in operon).
  • In the lac operon, i encodes a protein that binds to the operator.
  • In the presence of lactose, the repressor is inactivated.
  • Positive control is mediated by cAMP and CAP.

Eukaryotic Transcriptional Regulation

  • Eukaryotic gene regulation is more complex than prokaryotic regulation.
  • Eukaryotic DNA is organized into chromatin, which complicates protein-DNA interaction.
  • Transcription and translation are temporally and spatially separated.

Eukaryotic Chromatin Structure

  • DNA is wound around histone proteins & non-histone regulatory proteins to form nucleosomes.
  • Nucleosomes and histones complicate the process of transcription (restrict access of transcription machinery to the DNA)
  • Chromatin structure is selectively modulated to allow transcription.

Promoters and Enhancers

  • Promoters are DNA-binding sites for general transcription factors.
  • Promoters mediate the binding of RNA polymerase II to the promoter.
  • Enhancers are DNA-binding sites for specific transcription factors.
  • Enhancers act over long distances by bending DNA to form a loop to position the enhancer closer to the promoter.

Gene Regulation at Great Distances

  • Enhancers, like promoters, function by binding transcription factors that regulate RNA polymerase.
  • DNA looping allows a transcription factor bound to a distant enhancer to interact with proteins associated with the RNA polymerase/Mediator complex at the promoter.

Post-transcriptional Regulation

  • Regulation occurs after the mRNA is transcribed but before translation.

Eukaryotic Genes

  • Eukaryotic genes contain introns and exons.
  • Introns are removed, and exons are joined to create mature mRNA.

Pre-mRNA Splicing

  • Pre-mRNAs (primary RNA transcripts) are processed by removing introns and joining exons.
  • snRNPs and proteins, along with other factors, catalyze splicing.
  • Introns are excised from the molecule, and exons are ligated, or joined, together to form the mature mRNA.
  • Alternative splicing creates multiple mRNA variations (distinct forms).

Translation (mRNA to protein)

  • Ribosomes have three binding sites (P, A, and E).
  • Aminoacyl tRNA binds to the A site by pairing with the next mRNA codon.
  • An elongation factor (EF-Tu in prokaryotes, eEF1a in eukaryotes) brings the aminoacyl tRNA to the ribosome.
  • Peptide bonds are formed, and the polypeptide is transferred to the A site.
  • The uncharged tRNA is released from the P site.
  • Translocation occurs to position the next codon in the A site.

Post-translational Regulation

  • Regulation occurs after the protein is translated.

Lin-4 microRNA (miRNA)

  • Lin-4 is a microRNA that represses the translation of Lin-14.

Other miRNAs

  • As many as 1000 miRNAs are encoded in mammals.
  • Each can target hundreds of different mRNAs.

Protein Folding and Quality Control

  • Newly synthesized proteins fold into various possible shapes.
  • Misfolded proteins can form aggregates.
  • Correct protein folding is assisted by molecular chaperones.
  • Incorrectly folded proteins are targeted by the proteasome, which digests them.

Defects in Protein Folding

  • Defects in protein folding are responsible for many diseases.
  • Alzheimer's disease is associated with misfolded proteins and the accumulation of amyloid-beta plaques and tau tangles.

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Test your knowledge on essential molecular biology concepts, including DNA replication, translation, and protein folding. This quiz covers the key functions of DNA polymerase, the phases of the cell cycle, and more. Perfect for students of biology looking to reinforce their understanding of these fundamental processes.

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